Hopefully Citra will be useable soon so I can test all the indexes (If I remember right, X/Y/OR/AS use 2 bytes to determine index, so there's 65535 possible indexes. I may be wrong, though.) which will take FOREVER but it'll be something to do next summer.
You can already run Gen VI in a fork of Citra.
I already tried using Citra's gdbserver stub and an IDAPython script to modify the encounter tables in RAM, but it didn't work, I think because the addresses I had were for a later version of ORAS.
(Fun fact: you can already get code exec in ORAS using a malformed save file. I've been meaning to look into the Secret Base QR code parsing, because I don't think anyone else has, and I've also already looked into the QR codes of Tomodachi Life - I can take any Mii QR code, and then give it any full name, and make it come from any island address, then fix the checksum and encrypt the Tomodachi Life-specific portion.)